Enzyme chemistry classification

A third edition of the well-known book Enzymes by Dixon and Webb reflects the changes and developments which have occurred in the area of enzyme chemistry. Enzyme techniques, isolation, kinetics, classification, specificity, mechanisms, inhibition and activation, co-factors, structure, biosynthesis, and biology are all covered. Most of the material has been rewritten but, despite the wealth of new material included, the book retains the general form of the previous editions. 

Enzymes are classified in terms of the reactions which they catalyse and were formerly named by adding the suffix ase to the substrate or to the process of the reaction. In order to clarify the confusing nomenclature a system has been developed by the International Union of Biochemistry and the International Union of Pure and Applied Chemistry (see Enzyme Nomenclature , Elsevier, 1973). The enzymes are classified into divisions based on the type of reaction catalysed and the particular substrate. The suffix ase is retained and recommended trivial names and systematic names for classification are usually given when quoting a particular enzyme. Any one particular enzyme has a specific code number based upon the new classification. 

In this section, enzymes in the EC 2.4. class are presented that catalyze valuable and interesting reactions in the field of polymer chemistry. The Enzyme Commission (EC) classification scheme organizes enzymes according to their biochemical function in living systems. Enzymes can, however, also catalyze the reverse reaction, which is very often used in biocatalytic synthesis. Therefore, newer classification systems were developed based on the three-dimensional structure and function of the enzyme, the property of the enzyme, the biotransformation the enzyme catalyzes etc. [88-93]. The Carbohydrate-Active enZYmes Database (CAZy), which is currently the best database/classification system for carbohydrate-active enzymes uses an amino-acid-sequence-based classification and would classify some of the enzymes presented in the following as hydrolases rather than transferases (e.g. branching enzyme, sucrases, and amylomaltase) [91]. Nevertheless, we present these enzymes here because they are transferases according to the EC classification. 

The use of enzymes and whole cells as catalysts in organic chemistry is described. Emphasis is put on the chemical reactions and the importance of providing enantiopure synthons. In particular kinetics of resolution is in focus. Among the topics covered are enzyme classification, structure and mechanism of action of enzymes. Examples are given on the use of hydrolytic enzymes such as esterases, proteases, lipases, epoxide hydrolases, acylases and amidases both in aqueous and low-water media. Reductions and oxidations are treated both using whole cells and pure enzymes. Moreover, use of enzymes in sngar chemistiy and to prodnce amino acids and peptides are discnssed. 

All enzymes are named according to a classification system designed by the Enzyme Commission (EC) of the International Union of Pure and Applied Chemistry (IUPAC) and based on the type of reaction they catalyze. Each enzyme type has a specific, four-integer EC number and a complex, but unambiguous, name that obviates confusion about enzymes catalyzing similar but not identical reactions. In practice, many enzymes are known by a common name, which is usually derived from the name of its principal, specific reactant, with the suffix -ase added. Some common names do not even have -ase appended, but these tend to be enzymes studied and named before systematic classification of enzymes was undertaken. 

The names of the examples of textile-relevant enzymes follow the nomenclature of Duclaux from 1898, characterising an enzyme by the end-syllable ase , added to the name of the snbstrate that is split, synthesised or otherwise catalysed. As with all catalysts, enzymes reduce the activation energy of a specific reaction. The discovery of large qnantities of new enzyme systems afforded a more differentiated nomenclatnre, realised in 1964 by the International Union of Pure and Applied Chemistry (lUPAC) and the International Union for Biochemistry (lUB). In the new enzyme classification (EC) the first nnmber refers to one of the six main gronps and the following numbers to subgroups, for example EC 3.4.S.6, where 3 stands for hydrolases. ... 

The systematic name of an enzyme consists of two parts, the first originating from the equation, the second from the type of reaction catalyzed. In addition, according to the recommendations of the International Union of Pure and Applied Chemistry and the International Union of Biochemistry (1973), each enzyme bears a number from the international EC (Enzyme Classification) system, which reflects the main class, the subclass, and the subgroup. The number is completed by a special enzyme number. Thus, for example the EC number 1.1.3.4 of the enzyme with the trivial name glucose oxidase results from the following ... 

These enzyme libraries represent the beginning of a new set of biocatalyst tools for the synthetic chemist and were the first thermostable enzyme libraries developed specifically for synthetic chemistry applications in each of these chemical classifications. We have since been expanding the esterase and dehydrogenase libraries using a variety of new and diverse substrate compounds. As... 

In this review, the simple flavoenzymes will be discussed in groups according to the chemistry of a halfreaction - usually the biologically important half-reaction. This is different from the usual classifications based on the net reactions catalyzed or structural motifs. In addition to these enzymes, there are several flavoproteins that do not fit easily into any chemical group. These enzymes will be discussed at the end and include examples where more than one type of chemical conversion occurs, the enzyme contains additional prosthetic groups such as metal centers, or there is no evidence for the flavin being involved chemically in the reaction. 

The pr e-Woodwardhn era largely concerned itself with the collection and classification of synthetic tools chemical reactions suited to broad application to the constitutional construction of molecular skeletons (including Kiliani s chain-extension of aldoses, reactions of the aldol type, and cycloadditions of the Diels-Alder type). The pre- Woodwardian era is dominated by two synthetic chemists Emil Fischer and Robert Robinson. Emil Fischer was emphasizing the importance of synthetic chemistry in biology as early as 1907 [30]. He was probably the first to make productive use of the three-dimensional structures of organic molecules, in the interpretation of isomerism phenomena in carbohydrates with the aid of the Van t Hoff and Le Bel tetrahedron model (cf. family tree of aldoses in Scheme 1-6), and in the explanation of the action of an enzyme on a substrate, which assumes that the complementarily fitting surfaces of the mutually dependent partners are noncovalently bound for a little while to one another (shape complementarity) [31],... 

Much of this handbook is concerned with the how and why of crystallization and crystallizer design. This chapter will focus on the crystallization of one particular class of chemical compounds, namely the proteins. In the timeline of crystallization, protein crystallization is a newcomer. The first mention of protein crystal formation, roughly 150 years ago, involved crystallizing hemoglobin from the blood of various species (Lehman 1853 Reichert and Brown 1909 Debru 1983 McPherson 1991). This work was followed by the crystallization of a variety of proteins from plants to egg white (Sumner 1926). These early studies were pivotal in establishing that enzymes are proteins (Dounce and Allen 1988). The use of protein crystallization in purification and classification of biological chemicals resulted in the Nobel Prize for Chemistry being awarded to Sumner, Nothrop, and Stanley in 1946. 

Clavulanic acid is a mold product with only weak intrinsic antibacterial activity, but it is an excellent irreversible inhibitor of most (3-lactamases. It is believed to acylate the aotive site serine by mimioking the normal substrate. Hydrolysis occurs with some (3-lactamases, but in many cases, subsequent reactions ooour that inhibit the enzyme irreversibly. This leads to its classification as a mechanism-based inhibitor (or so-oalled suicide substrate). The precise chemistry is not well understood (Fig. 38.18), but when clavulanio acid is added to ampicillin and amoxicillin preparations, the potenoy against (3-lactamase-produoing strains is markedly enhanced. 

Molecular Biology on the nomenclature and classification of enzyme-catalyzed reactions by Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, available online at www.chem.qmul.ac.uk/iubmb/ enzyme/ NC-IUBMB, Symbolism and terminology in enzyme kinetics Nomenclature Committee of the International Union of Biochemistry, available online at www.chem.qmul.ac.uk/iubmb/kinetics/ prepared by G.P. Moss department of chemistry. Queen Mary University of London, U.K., 1981. 

For a simple introduction to the chemistry of enzyme action, see Williams (1969), for a list of enzymes with discussion, see Dixon and Webb (1979), and for a multivolume work on enzymes, see Boyer (1970-1983). Isoenzymes and isofunctional enzymes were discussed in Section 4.2. For the classification of enzymes, see International Union of Biochemistry (1978). 

Table 2.4. Systematic classification of some enzymes of importance to food chemistry...

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